If they should appear in different apparatus you could use the bigfoot package (Gonzalo was faster...):
\documentclass{article}
\usepackage{bigfoot}
\DeclareNewFootnote{A}
\DeclareNewFootnote{B}
\renewcommand\thefootnoteB{(\arabic{footnoteB})}
\textheight=80pt% just for the example
\begin{document}
Text text\footnoteA{Group one.} text.\footnoteB{Group two.}
Text text\footnoteA{Group one.} text.\footnoteB{Group two.}
\end{document}
If they must appear in the same apparatus you could use the sepfootnotes package. You then have to declare the actual footnote content separately, though.
\documentclass{article}
\usepackage{sepfootnotes}
\newfootnotes*{A}
\newfootnotes*{B}
\renewcommand\theBmark{(\arabic{Bnote})}
\Anotecontent{first}{Group one.}
\Anotecontent{second}{Group one.}
\Bnotecontent{first}{Group two.}
\Bnotecontent{second}{Group two.}
\textheight=80pt% just for the example
\begin{document}
Text text\Anote{first} text.\Bnote{first}
Text text\Anote{second} text.\Bnote{second}
\end{document}
Edit:
If you want the separate groups to be numbered consecutively you need to do some redefinitions. Here's an example using the sepfootnotes package (it's analogous for bigfoot):
\documentclass{article}
\usepackage{sepfootnotes}
\newfootnotes*{A}
\newfootnotes*{B}
\let\BnoteOrig\Bnote
\renewcommand\Bnote{\stepcounter{Anote}\BnoteOrig}
\renewcommand\theBmark{(\arabic{Anote})}
\Anotecontent{first}{Group one.}
\Anotecontent{second}{Group one.}
\Bnotecontent{first}{Group two.}
\Bnotecontent{second}{Group two.}
\textheight=80pt% just for the example
\begin{document}
Text text\Anote{first} text.\Bnote{first}
Text text\Anote{second} text.\Bnote{second}
\end{document}
